Letter | Published:

Atomic-resolution dynamics on the surface of amyloid-β protofibrils probed by solution NMR

Nature volume 480, pages 268272 (08 December 2011) | Download Citation

Abstract

Exchange dynamics between molecules free in solution and bound to the surface of a large supramolecular structure, a polymer, a membrane or solid support are important in many phenomena in biology and materials science. Here we present a novel and generally applicable solution NMR technique, known as dark-state exchange saturation transfer (DEST), to probe such exchange phenomena with atomic resolution. This is illustrated by the exchange reaction between amyloid-β (Aβ) monomers and polydisperse, NMR-invisible (‘dark’) protofibrils, a process of significant interest because the accumulation of toxic, aggregated forms of Aβ, from small oligomers to very large assemblies, has been implicated in the aetiology of Alzheimer’s disease1,2,3,4,5,6. The 15N-DEST experiment imprints with single-residue-resolution dynamic information on the protofibril-bound species in the form of 15N transverse relaxation rates (15N-R2) and exchange kinetics between monomers and protofibrils onto the easily observed two-dimensional 1H–15N correlation spectrum of the monomer. The exchanging species on the protofibril surface comprise an ensemble of sparsely populated states where each residue is either tethered to (through other residues) or in direct contact with the surface. The first eight residues exist predominantly in a mobile tethered state, whereas the largely hydrophobic central region and part of the carboxy (C)-terminal hydrophobic region are in direct contact with the protofibril surface for a significant proportion of the time. The C-terminal residues of both Aβ40 and Aβ42 display lower affinity for the protofibril surface, indicating that they are likely to be surface exposed rather than buried as in structures of Aβ fibrils7,8,9,10, and might therefore comprise the critical nucleus for fibril formation11,12. The values, however, are significantly larger for the C-terminal residues of Aβ42 than Aβ40, which might explain the former’s higher propensity for rapid aggregation and fibril formation13,14.

Access optionsAccess options

Rent or Buy article

Get time limited or full article access on ReadCube.

from$8.99

All prices are NET prices.

References

  1. 1.

    & Are amyloid diseases caused by protein aggregates that mimic bacterial pore-forming toxins? Q. Rev. Biophys. 39, 167–201 (2006)

  2. 2.

    & Aβ oligomers – a decade of discovery. J. Neurochem. 101, 1172–1184 (2007)

  3. 3.

    Structural classification of toxic amyloid oligomers. J. Biol. Chem. 283, 29639–29643 (2008)

  4. 4.

    & Mechanisms of disease: Alzheimer’s disease. N. Engl. J. Med. 362, 329–344 (2010)

  5. 5.

    et al. Structural conversion of neurotoxic amyloid-β1–42 oligomers to fibrils. Nature Struct. Mol. Biol. 17, 561–567 (2010)

  6. 6.

    et al. High-molecular-weight beta-amyloid oligomers are elevated in cerebrospinal fluid of Alzheimer patients. FASEB J. 24, 2716–2726 (2010)

  7. 7.

    et al. A structural model for Alzheimer’s β-amyloid fibrils based on experimental constraints from solid state NMR. Proc. Natl Acad. Sci. USA 99, 16742–16747 (2002)

  8. 8.

    et al. 3D structure of Alzheimer’s amyloid-β(1–42) fibrils. Proc. Natl Acad. Sci. USA 102, 17342–17347 (2005)

  9. 9.

    , , & Molecular structural basis for polymorphism in Alzheimer’s β-amyloid fibrils. Proc. Natl Acad. Sci. USA 105, 18349–18354 (2008)

  10. 10.

    , & Experimental constraints on quaternary structure in Alzheimer’s β-amyloid fibrils. Biochemistry 45, 498–512 (2006)

  11. 11.

    , , & Determining the critical nucleus and mechanism of fibril elongation of the Alzheimer’s Aβ1–40 peptide. J. Mol. Biol. 365, 535–550 (2007)

  12. 12.

    & Mechanisms of protein fibril formation: nucleated polymerization with competing off-pathway aggregation. Biophys. J. 94, 379–391 (2008)

  13. 13.

    , & The carboxy terminus of the beta amyloid protein is critical for the seeding of amyloid formation: implications for the pathogenesis of Alzheimer’s disease. Biochemistry 32, 4693–4697 (1993)

  14. 14.

    , , , & NMR studies in aqueous solution fail to identify significant conformational differences between the monomeric forms of two Alzheimer peptides with widely different plaque-competence, Aβ(1–40)(ox) and Aβ(1–42)(ox). Eur. J. Biochem. 268, 5930–5936 (2001)

  15. 15.

    , , & Kinetics of amyloid β monomer-to-oligomer exchange by NMR relaxation. J. Am. Chem. Soc. 132, 9948–9951 (2010)

  16. 16.

    et al. Elucidating amyloid β-protein folding and assembly: a multidisciplinary approach. Acc. Chem. Res. 39, 635–645 (2006)

  17. 17.

    et al. High-resolution atomic force microscopy of soluble Aβ42 oligomers. J. Mol. Biol. 358, 106–119 (2006)

  18. 18.

    Reassessing the amyloid cascade hypothesis of Alzheimer’s disease. Int. J. Biochem. Cell Biol. 41, 1261–1268 (2009)

  19. 19.

    , , , & Solid-state NMR spectroscopic investigation of Aβ protofibrils: implication of a β-sheet remodeling upon maturation into terminal amyloid fibrils. Angew. Chem. 50, 2837–2840 (2011)

  20. 20.

    et al. Solution NMR studies of the Aβ(1–40) and Aβ(1–42) peptides establish that the met35 oxidation state affects the mechanism of amyloid formation. J. Am. Chem. Soc. 126, 1992–2005 (2004)

  21. 21.

    & Aβ42 is more rigid than Aβ40 at the C terminus: implications for Aβ aggregation and toxicity. J. Mol. Biol. 364, 853–862 (2006)

  22. 22.

    Reaction rates by nuclear magnetic resonance. J. Chem. Phys. 28, 430–431 (1958)

  23. 23.

    , & Simulations of NMR pulse sequences during equilibrium and non-equilibrium chemical exchange. J. Biomol. NMR 18, 49–63 (2000)

  24. 24.

    , , & Amyloid-β forms fibrils by nucleated conformational conversion of oligomers. Nature Chem. Biol. 7, 602–609 (2011)

  25. 25.

    et al. Molecular recycling within amyloid fibrils. Nature 436, 554–558 (2005)

  26. 26.

    , , , & Structure and intermolecular dynamics of aggregates populated during amyloid fibril formation studied by hydrogen/deuterium exchange. Acc. Chem. Res. 43, 1072–1079 (2010)

  27. 27.

    , & Measurement of methyl group motional parameters of invisible, excited protein states by NMR spectroscopy. J. Am. Chem. Soc. 131, 12745–12754 (2009)

  28. 28.

    & Accuracy of optimized chemical-exchange parameters derived by fitting CPMG R2 dispersion profiles when R20aR20b. J. Biomol. NMR 34, 209–219 (2006)

  29. 29.

    , , , & The proteasome antechamber maintains substrates in an unfolded state. Nature 467, 868–871 (2010)

  30. 30.

    , & Mechanism of coupled folding and binding of an intrinsically disordered protein. Nature 447, 1021–1025 (2007)

  31. 31.

    , & Measurement of 13C longitudinal relaxation using 1H detection. J. Magn. Reson. 73, 375–379 (1987)

  32. 32.

    et al. NmrPipe – a multidimensional spectral processing system based on Unix pipes. J. Biomol. NMR 6, 277–293 (1995)

Download references

Acknowledgements

We thank R. Tycko for discussions, D. Baber, D. Garrett and M. Cai for NMR technical assistance, F. Shewmaker for performing dot blots, and W. Qiang, B. Chen and K. Thurber for assistance with atomic force microscopy and electron microscopy imaging. This work was supported by the intramural program of the National Institute of Diabetes and Digestive and Kidney Diseases/National Institutes of Health and the AIDS Targeted Antiviral Program of the Office of the Director of the National Institutes of Health (to G.M.C.).

Author information

Affiliations

  1. Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland 20892-0520, USA

    • Nicolas L. Fawzi
    • , Jinfa Ying
    •  & G. Marius Clore
  2. Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland 20892-0520, USA

    • Rodolfo Ghirlando
  3. National Institute of Dental and Craniofacial Research, National Institutes of Health, Bethesda, Maryland 20892-0520, USA

    • Dennis A. Torchia

Authors

  1. Search for Nicolas L. Fawzi in:

  2. Search for Jinfa Ying in:

  3. Search for Rodolfo Ghirlando in:

  4. Search for Dennis A. Torchia in:

  5. Search for G. Marius Clore in:

Contributions

All authors contributed extensively to the work described in this paper.

Competing interests

The authors declare no competing financial interests.

Corresponding author

Correspondence to G. Marius Clore.

Supplementary information

PDF files

  1. 1.

    Supplementary Information

    The file contains Supplementary Text and Data, Supplementary Figures 1-12 with legends, Supplementary Table 1 and additional references.

About this article

Publication history

Received

Accepted

Published

DOI

https://doi.org/10.1038/nature10577

Further reading

Comments

By submitting a comment you agree to abide by our Terms and Community Guidelines. If you find something abusive or that does not comply with our terms or guidelines please flag it as inappropriate.